AMBER Archive (2009)
Subject: Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old)
From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Tue Jul 28 2009 - 06:59:51 CDT
Dear Ashish Runthala,
> you can do with these grep commands, but it will do for all, and not
> all protons are insignificant. Remember here, that such protons seems
> weak bonds, but even then they are responsible for the stability of
> the overall confirmation. Check the structure in leap and protonate in
> a standard fashion, there, after removing the errors and warnings in
> My advise is to properly verify the structure before stepping further.
> What you are working it out for by the way?
As said Bill egrep is perfect for that.
You could egrep using specific hydrogen names.
egrep -v "HB2|HB3" my.pdb > my_no-HB2HB3.pdb
egrep -v "HA2|HA3|HB1|HB2|HB3" my.pdb > my_no-selected-H.pdb
> On Mon, Jul 27, 2009 at 9:17 AM, Bill Ross<ross_at_cgl.ucsf.edu> wrote:
>>> how can I proceed to remove proton in protein
>> % egrep -v H my.pdb > my_no_h.pdb
AMBER mailing list